Hi,
Many thanks, Justin, for your time. As a first try, I am going ahead with
your proposed option (1): make my own local copy of spce.itp and adjust the
call (the #include) in the topology file. I have zeroed the charges in this
local copy of spce.itp and tried to prepare for energy minimization, using
grompp:
grompp -f minim.mdp -c water_processed.gro -p water.top -o em.tpr -po
emout.mdp
When I do this, I get a warning message:
------
WARNING 1 [file minim.mdp]:
You are using full electrostatics treatment PME for a system without
charges.
This costs a lot of performance for just processing zeros, consider using
Cut-off instead.
------
which leads to a fatal error. I can work around this fatal error by setting
-maxwarn to 1, and this is what I am going to try now. At this point, I am
not too concerned about speed because my system is small and my simulation
is short. But, just out of curiosity, what do you think that the above
warning is suggesting that I do instead? As it stands now, in my .mdp file,
I have (among other things) the following:
------
...
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
optimize_fft = yes
...
------
I guess that it is suggesting that I NOT use coulombtype = PME, and instead
use coulombtype = Cut-off, as referred to on this page:
Thank you kindly!
Andrew DeYoung
Carnegie Mellon University
--
Andrew DeYoung wrote:
Hi,
I am running NVE simulations of a system of 1000 water molecules. I am
attempting to run analogous simulations on Gromacs 4.5.4 and also on
another
MD program. Once finished, I will compare the results of the two
programs.
It was suggested to me that to compare the results of the two programs in
a
step-by-step manner, as a first step I should run the simulations with the
electrostatics (both short-range and long-range interactions) turned off.
In other words, run the simulations considering only Lennard-Jones
interactions. My question is, what is the best way to do this in Gromacs?
A (very much more experienced) colleague suggested that I "turn off
electrostatics" by simply setting all the charges to zero. However, when
I
look into the topology and structure files, I see some surprising (to me)
things -- the charges do not appear to be specified in the .top and .gro
files.
To back up, I will first try to explain my system. I have a PDB file
specifying 1000 water molecules that someone gave me. This PDB file looks
like the following:
TITLE water
REMARK THIS IS A SIMULATION BOX
CRYST1 47.100 47.100 47.100 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 OW SOL 1 -21.177 -21.195 -21.179 1.00 0.00
ATOM 2 HW1 SOL 1 -21.671 -21.195 -22.083 1.00 0.00
ATOM 3 HW2 SOL 1 -21.863 -21.195 -20.412 1.00 0.00
ATOM 4 OW SOL 2 -16.467 -21.195 -21.179 1.00 0.00
ATOM 5 HW1 SOL 2 -16.961 -21.195 -22.083 1.00 0.00
ATOM 6 HW2 SOL 2 -17.153 -21.195 -20.412 1.00 0.00
...
And so on. According to the PDB file format specification
(http://www.wwpdb.org/format/sect9.html), the last two columns in my file
correspond to the occupancies and temperature factors, respectively, of my
atom. So, evidently, partial charges on the oxygen and hydrogens are not
specified in this PDB file.
Next, I execute the command:
pdb2gmx -f water.pdb -p water.top -i water.itp -o water_processed.gro
And, when prompted, I choose the OPLS-AA force field and the SPC/E water
model. Apparently, Gromacs recognizes from my PDB file that my system
contains water (and only water). Alternatively, I could have created a
topology file manually, without pdb2gmx, by simply creating a .top file
containing:
------
#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/spce.itp"
[ system ]
water
[ molecules ]
SOL 1000
------
and then simply feed grompp the topology file and the original PDB file
when
preparing for a dynamics run (pdb2gmx, I understand, is meant for chains
rather than multiple molecules). But, in any case, I took the long road
and
used pdb2gmx to create the .top topology and a .gro coordinate file.
What surprises me (a novice in Gromacs and MD in general), though, is that
it seems that neither the .top file nor the .gro file contains any
reference
to the charges on the oxygens and hydrogens in this water-only system.
For
example, my .top file contains:
------
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
; Include water topology
#include "oplsaa.ff/spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "oplsaa.ff/ions.itp"
[ system ]
; Name
water
[ molecules ]
; Compound #mols
SOL 1000
------
And, my .gro file contains, for example:
------
water
3000
1HOH OW 1 -2.118 -2.119 -2.118
1HOH HW1 2 -2.167 -2.119 -2.208
1HOH HW2 3 -2.186 -2.119 -2.041
2HOH OW 4 -1.647 -2.119 -2.118
2HOH HW1 5 -1.696 -2.119 -2.208
2HOH HW2 6 -1.715 -2.119 -2.041
...
4.71000 4.71000 4.71000
------
So, as far as I can tell, neither my .top nor my .gro file specify the
charges on the atoms. I guess that this means that the charges on the
atoms
are only specified in the spce.itp file. When I find and open the
spce.itp
file, I see:
------
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1 SOL OW 1 -0.8476
2 opls_117 1 SOL HW1 1 0.4238
3 opls_117 1 SOL HW2 1 0.4238
#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#endif
------
So, there the charges are specified: -0.8476 on the oxygen and 0.4238 on
each hydrogen. Coming back to my original goal--to "turn off
electrostatics" by zeroing the charges--I could in principle just set the
charges in this .itp file to 0. However, on our cluster, this file
appears
to be READ ONLY. So to change the charges to 0, I need to see if I can
get
permission from our administrator.
That would be a terrible idea. It would affect anyone who uses that file,
and
then surprise! their entire simulation is worthless because the charges are
not
there :)
Based on my story above, my questions are:
1. Is there a better way to "turn off electrostatics"--without modifying
the spce.itp file?
There are several options:
1. Don't mess with the system-wide spce.itp file. Make your own local copy
and
alter it there. Adjust the call in the .top to some location where it will
be
found (which you can set with the "include" keyword in the .mdp file, if
necessary).
2. Don't mess with topologies at all and instead use the free energy code
with,
e.g.:
couple-moltype = SOL
couple-lambda0 = vdw
couple-moltype = (either vdw or none)
init-lambda = 0
Then don't both with any other lambda values, since you don't care about the
free energy of some transformation of the system, just the energy value of
the
Hamiltonian under these conditions. This is a very roundabout way of
accomplishing your task.
3. Use a simpler system like a noble gas, which has no charges to begin
with.
2. Why does it seem that charges are not specified in the .top and .gro
files? Is this just because I am boringly simulating only a solvent, and
the topology file tells Gromacs to look in spce.itp when simulating the
water molecules?
Charges *are* specified in the .top file, albeit indirectly. The #include
statement is a C preprocessor term that literally means "cut and paste the
contents of the included file right here." If you use grompp -pp to get the
post-processed topology you will see. The #include statements are there for
convenience, so you don't have to copy and paste a water topology for every
single simulation, which would be horrendously annoying for most of us.
Most
other "normal" (i.e. protein-containing) topologies have all the information
for
the protein listed explicitly (see my tutorial, or probably any other, for a
complete description).
The .gro file does not contain charges because it is a coordinate file. It
has
atom and residue names and numbers, coordinates, and (optionally)
velocities.
-Justin
Thank you very much for your time!
Andrew DeYoung
Carnegie Mellon University
